Rory Is Missing
by d4nc3-f0r-th3m
Summary: Rory has been kidnapped leaving Amy and the Doctor to try and find him. What happens when the Doctor and Rory's true feelings come to light?  11/Rory, and some Rory/Amy.  I own nothing.
1. Chapter 1

He doesn't know where he is and it's dark. Someone is whispering from far off that it will all be alright if he just wakes up.

But he can't wake.

He's trapped forever in this nothingness not even rememebering who he is. A familiar face drifted through his subconscious. The way his face looked when he laughed, all of his wisdom and knowledge. His two hearts beating in unison for more than a thousand years.

The Doctor. He loves The Doctor, he thought before losing all consciousness.

* * *

><p>"Doctor!" Amy sobbed into his ear as he restrained her. "They took him! Those idiots took him!"<p>

"I see that pond," he responded irritably.

"Go get him back then!"

"Amy!" The Doctor said sternly taking a firm hold of her shoulders before shaking her. "If you want him back you need to get a hold of yourself so I can think."

"How can I think when my husband was just kidnapped, Doctor?" She asked, her flame colored hair wild her stress. "You act like he isn't even important to you!"

"He is important to me Amy! Don't you dare say he isn't!" He snapped leaving her speechless and blinking.

"Then get me back my husband." She told him as she walked towards the TARDIS.

After she had left he turned and punched the brick wall, anger wafting off of him. He leaned his forehead agaisnt the cool bricks as he looked at his bloody knuckles.

"Of course he's important to me." He whispered, pain engulfing his two hearts in waves. As he made his way back to TARDIS he looked up at the four suns of Darblix. They had come there to have fun, see the sights, swim some. All the Doctor wanted now was to have Rory back beside him unharmed and safe. "Why is it always you Rory?"

Opening TARDIS' blue doors he stepped inside. "Why did they take him?" Amy asked as soon as she saw him.

"If I knew we'd already have him back by now."

"But you don't know why." She stated, heartbreak filling her voice. "I don't want to lose him again, Doctor."

"I don't ethier Amy." He mumbled as he twisted and turned knobs on TARDIS' control panel. "Go to bed Amy, we'll figure it out in the morning."

She opened her mouth to say something but the Doctor put his hand up to stop her. "Sleep Amy, you need to get some sleep."


	2. Chapter 2

Okay, really short chapter. Sorry.D:  
>I own nothing.<p>

I wish I did, but I don't.

Reviews are always lovely.3

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><p>The Doctor sat at a table in TARDIS' kitchen stirring his tea. He could remember everything that Rory did when he was nervous, upset, happy. It didn't matter what it was, The Doctor could just remember his so well.<p>

They used to sit her at night when Amy was asleep and just talk. Rory would talk about his days as a Roman and how different it was. The Doctor would sit there and tell of his long travels through all of space and time. All the while he would just wonder how Rory could be so brilliant.

"Where are you Rory?" He whispered taking a sip of his tea.

* * *

><p>"Wh-Where am I?" Rory Williams asked looking around franticly.<p>

"You are in the Institute." A voice answered coming from the darkness.

"Why am I here?"

"Because we picked you for the testing."

"As a lab rat?" Rory's voice squeaked as he looked around in the darkness. He couldn't make out the vaguest of shapes. "Why me?"

"Because you were here when we needed someone. We must thank you for dropping by when you did."

Hands grabbed the tall human by the shoulders and yanked him upward.

"Testing time." It's voice dripped with excitement as Rory was drug away into a lighted room, leaving him struggling against his captures.

The room was blinding compared to the blackness that had surrounded him. Operating tables were set up around the room, each with someone or something, on it. Only one table was open, it was the one Rory was being pulled towards.

"DOCTOR!" Was Rory's last words before he was strapped down and knocked unconscious.


	3. Chapter 3

Amy lay awake in their room hugging Rory's pillow to her chest. She never showed him the love he deserved, she thought as silent tears dripped down her face. She just wanted to have his arms around her again as they slept, to have that secure feeling of him keeping her safe.

She buried her face into his pillow inhaling his scent, her heart aching for him to whisper he loves her like he always did before bed. But he's not here anymore, he's gone, kidnapped, possibly being tortured while she lays there helpless.

She needs Rory more than ever.

* * *

><p>Rory's screams weren't heard over the manic laughter as he was hit over and over. He could hardly get a breath before another hard blow hit him. He stopped struggling after they had taken out a whip laced with tiny rows of knives.<p>

Finally, after hand out of relentless beating, it stopped.

"How," he gasped trying to regain his composure, "is this testing?

"We're testing how long it takes for your friends to come to your rescue, human. Unless you die here first."

"Why does it matter if they come and get me?"

"You ask so many questions. It's very unbecoming." It said with disgust as it sighed from somewhere near Rory's right ear.

Rory swung his head to the side to see it's face; but it was just air upon air. "Why can't I see you?

"Because you don't want to see us, so you don't. You're still a scared little boy, Rory."

* * *

><p>The Doctor stared at TARDIS' screen, his brows scrunching together in frustration. "Amy! Can you remember anything from Rory's kidnappers?"<p>

"N-No," she whispered covering her face with her hands. "I don't remember anything.""You wouldn't, shouldn't, remember anything Amy."

"Why not? I hate feeling like this. Feeling so helpless."

"Because when I came out of the store, you were unconscious. They didn't want you finding out what they were because if you did, they knew I'd come." The Doctor answered running his hands through his hair.

"I don't remember being hit." She answered looking slightly confused.

"They didn't hit you physically. Mentally. They hit you with their minds. Their telepathic!" He ran around the console, hope bursting in his eyes. "We have somewhat of a lead, Pond!"

"Let's hope it gets us somewhere."

"Let's never stop hoping. Hope is needed for human life."

"Yada, yada, yada." The red head rolled her eyes. "You'll say some more wisdom crap that doesn't help us get any closer to finding Rory."

"Don't act like I'm not worried, Amy."

"Then show that you're worried for once. Just once I'd like to see you go crazy with feelings." She said as she stormed away leaving the Doctor hurt.

"I can't show my feelings, if I do, I'll lose my control." He whispered wiping a tear from his right cheek.


	4. Chapter 4

Rory turned his head and spit into the white tile, blood splattering. "I-Can't-Take-Anymore." He gritted out between his teeth, taking short shallow breaths. He ached all over and felt like he had been put through a blender on chop.

"Are you sure?" It hissed in his face. He didn't bother opening his eyes because he knew he wouldn't see anything.

"Take him back to the cell." It barked at one of the other things in the room.

His eyes opened at that and looked around franticly. He didn't want to go back to the dark. The dark brought up bad memories he didn't want to think about. Things that shouldn't have happened, he shouldn't have done, things he hadn't even told the Doctor or Amy about and they were his best friends. His time as a Roman was fun, but more than anything, it was dark. He had a dark past that made his heart hurt at the thought of _him_ finding out.

The guilt weighed on him like lead everyday and he couldn't stand it.

The straps holding him down loosened as he was yanked off by his upper arm. Pain exploded behind his eyes as he muffled the moan that rose to his lips. He thought of the Doctor because that was the only thing keeping him going. Rory needed the Doctor. He needed that mad man's secret smile that was reserved just for him. He needed the Doctor's gentle pats to reassure Rory that everything was going to be alright. He didn't think about what Amy would say if she knew how in love he was with him. He just let himself drown in memory after memory of the Doctor.

* * *

><p>The Doctor loosened his bow tie after shoving his jacket to a corner of the control room. He tried to keep the tears from flowing but it was like trying to stop a flood. He leaned over the console, buttons blurring as tears drowned them. Turning he slid down the wall as sob after sob wracked his body.<p>

Rory. His Rory was somewhere being beaten and he had no power to stop it. When did he become so weak and useless? "Rory, I swear, I'll find you."

* * *

><p>Amy pulled on one of Rory's old sweatshirts sniffling. The tears never really stopped when she was alone, but with the Doctor, she had to put on a brave face. She knew what she had said to him was wrong, she knew she hurt him. She just didn't have it in her to care right now, but she knew it'd come back and bite her in the butt later.<p>

Amy laid back against his pillow and picked up the picture of him, the Doctor, and her. Her fingers trailed the edges of his smiling face. She missed his carefree smile, his bed head, the way he laughed. She missed him.

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><p>Really short I know, I know. Please don't come after me with torches.<br>Review, my lovelys.[:


	5. Chapter 5

The Doctor paced the control room, hands behind his head. Telepathic. He needed more information on them then that to find them. What did they look like? How did they talk? Frustrated he threw the notebook in his hand against the wall. "What do I have to do?"

The Doctor was going to lose his mind. Well, more than it was already gone. He had to find Rory. He wouldn't be able to live with himself if he lost the clumsy human. He'd already lost Rose and so many others. He couldn't lose another. It'd likely be the death of him. Watching the computer screen he scratched his head. There was something missing. Something poking at the back of his mind screaming "Look! Look at me!" Yet he couldn't quite focus on it.

Letting out a frustrated scream he kicked the coat rack in the corner sending it flying across the room. "Why now? Why so soon?" He yelled at the silent room pushing his hands through his hair. "Why when I was getting so close…So used to him."

Of course no one answered. There was only him in the room. Amy had gone to bed, tired and upset. Amelia Pond. The girl who waited. The girl who led him to Rory. The one who was married to him. It was wrong to love him but the Doctor couldn't help wanting to be in the presence of him. When did he become so vulnerable?

"Rory," he whispered closing his eyes. "I swear when I find you you're going to be in for a big surprise, mate."

* * *

><p>Rory could hear laughter in the darkness coming from all sides. He could act fearless all he wanted, but when reality came crashing down he was a coward. He didn't deserved to be saved by the Doctor. If the Doctor knew the things he'd done he wouldn't find him worthy either. He'd take him back home and leave him. Amy would leave him. She was always kind of in love with the mad man. But could he blame her? He was too. He had been since he popped out of his bachelor cake the night he asked him to travel the universe. Rory had only ever loved two people in his whole life. Amy and the Raggedy Doctor. Amy's Raggedy Doctor. Rory's friend.<p>

At first Rory had felt disdain for the man who filled his wife's head with fantasy. After a while he realized it as jealously. Jealousy for Amy's relationship with him. Rory wanted to have that sort of closeness with him. It was impossible though, He would never be the Doctor's choice. It was most likely Amy or a former companion.

_Clang!_

Rory's heart jumped into his throat as he could hear the cell doors clang open. Someone was screaming. It was a man. American. A muffled thud sounded as the person was thrown in front of Rory. "I don't understand why I'm being studied! I'm human! There's nothing special about me."

"You are a friend of the Doctor's. The immortal one we've heard of. Captain Jack Harkness. You must be studied."

* * *

><p>"Amelia!" The Doctor yelled waking Amy with a start. She had just fallen asleep. "I know who took him! I know who took our beautiful Rory!"<p>

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><p>It's been forever. I know. I am so sorry. I've just been so caught up with school work and sports I haven't had time. That's no excuse though. It's really short but at least the Doctor is getting somewhere! And now we have Captain Jack Harkness our favorite bisexual time traveler. Review and favorite please, lovelys.<p> 


	6. Chapter 6

Rory looked at the American called Jack. "You know the Doctor?"

"Yeah, traveled with the mad man a few times." He answered brushing off the front of his shirt. "You know 'im?"

"I was traveling with him." Rory answered wiping sweat at the sweat on his brow coming away with blood. "Recently."

"How long have you been here?"

"A day I think," Rory answered letting out a shuddering breath.

"And they've already beat you down that bad?" Jack asked him leaning against the wall next to Rory.

"They don't seem to like me too well." Rory snorted turning to look at him. "I've died once a long time ago. No one remembered me. I don't really remember the dying part, it's a little fuzzy. I do remember the nothingness."

"I've died many times…How'd it happen?"

"Pushed the Doctor out of the way and took the shot myself. Then I got taken by the crack, erased from time forever." Rory told him sadly thinking of all the Doctor had sacrificed for the world to be right again. "That was until I came back though. Amy had remembered me."

"And you came back alright?" Jack asked, seeming oddly nervous for the answer.

"Well, no, I was plastic. A plastic Centurion in fact. The last Centurion."

"Well, you're not plastic now."

"The Doctor stopped it all. He erased himself from time to save the universe, save Amy and me." Rory said thinking back to seeing the crazy Doctor he loved climb into the Pandorica and fly away.

"He's dead? Gone?" Jack sounded heartbroken.

"Of course not," Rory told him with a look. "Amy remembered him and he came back. "We've been traveling with him ever since."

"Do you love him?"

Jack's question had caught Rory off guard. What did it matter? "Who are you Jack?"

"Captain Jack Harkness," Jack announced shaking Rory's hand briefly. "Traveled with the Doctor too and became immortal."

"How?" Rory was astonished.

"It's complicated," Jack sounded sad all of a sudden.

"Time for more tests, Rory." The cold voice slipped down his spine.

"I've been in here for ten bloody minutes." He shouted knowing if he went back in there he would surly die.

* * *

><p>The Doctor pulled out his sonic screwdriver and ran it over the locked door. <em>Click!<em> He slipped inside keeping to the shadows. He had told Amy it was too dangerous and had made her stay in the TARDIS. In all honesty, he was just selfish. The only reason the Doctor had made her stay was because he wanted to save Rory by himself. To see Rory first.

A scream sounded through the corridor. Rory's scream.

Adjusting his crooked bow time he strolled into the room looming in front of him. He couldn't believe what he saw in front of him. Rory, clothes clinging to his bloody skin by slivers, was strapped to a table being cut by a scalpel. The thing holding the scalpel was on of The Men. One of the most feared species in the universe. They could talk but preferred telepathic communication. No one could see them unless they wanted to be seen or you weren't scared. But the Doctor was scared. Scared for Rory's life. The powers of The Men were unknown which frightened him further more.

Tall, pale, and skinny it turned it's hollow face toward the Doctor. It's eyelids were sewn shut along with it's lips. A long low hiss sounded throughout the Doctor's head. Rory looked pale and unconscious. The slow rise and falls of his chest reassured him that Rory was still breathing. Still alive.

"Hello, I'm the Doc-"

_I know who you are, Time Lord. _It hissed inside his head. _You are here for the human, are you not?_

"Why else would I be in a place like this? Unless I was wanting to have some surgery. Which I do not." The Doctor moved closer to the table eyes on Rory. "Why him? Out of all the humans populating this planet _why him_? Just to spite me?"

"Spite? No, we are more professional than that Doctor. You underestimate us."

"Why is he being beaten? What kind of sadistic test is that?" The Doctor felt flowing though his veins like scalding lava.

"We're testing you. Your reactions." It walked toward gun hands folded. Blood was smeared across it's white knuckles.

"For what?" He couldn't keep the malice out of his voice.

"To destroy you, Doctor, and rip apart time and space."


End file.
